AT LEAST WE'RE IN THE DARK TOGETHER
by lakota1954
Summary: This is just a start to fill in some of the missing scenes in Agents of Shield since Skye and Coulson embark on their new quest in the episode YES MEN.
1. Chapter 1

AT LEAST WE'RE IN THE DARK TOGETHER

Coulson's breathing began to return to normal as he sagged against the wall of the med cube. He couldn't believe what he'd just said to Skye, and he was astounded at her reaction. She hadn't yelled at him. She hadn't held him accountable for the horrible thing he'd done to her. Hell, she had actually thanked him for saving her life. He tried to think logically instead of emotionally. Maybe she was just so grateful to him for giving her a place to stay, a family of sorts. Was she just agreeing with him because he was her boss and she didn't want to lose her job?

_God, I'm as bad as Fury. I've done this horrible thing to her and now I'm expecting her full obedience._

He looked furtively at Skye and saw her staring at him intently. To her, he looked like an exhausted rabbit unable to shake the wolf off his trail.

"A.C. sit down," she said softly as she moved over on the bed. He was gripped with uncertainty for a moment, but his tired body made the decision for him, and he sagged down next to her. She laid a gentle hand on his arm and sighed.

"Those wheels in your head are spinning so fast I think I can see smoke coming out of your ears. What's wrong?" she said gently. He closed his eyes and tried to make his racing thoughts slow down. Secrets and lies tangled in a vast web of confusion in his head. He no longer had the steady sense of what was right and what was wrong. He wasn't sure anymore. How could he explain this with any degree of clarity? Skye's hand moved to rub up and down on his back and the feeling actually calmed him. It had been so long since he had experienced any sort of physical comfort.

_Not since, Beth. _ He almost smiled at the thought of his cellist girlfriend until another thought swirled to the forefront.

_Was she even real? Did Fury implant her as well?_ He shuddered. Skye leaned closer, and placed her other hand on his chest, effectively holding him.

"Skye, I'm… messed up. I can't think like I used to. Everything… everybody is no longer what I've always thought them to be. Even me. I'm not sure you should even be agreeing to work with me. What if seeking these answers is wrong?" He ducked his head, embarrassed and ashamed.

_She's thinking I've gone over the edge. Maybe I have. _He thought desperately. Skye began talking in a firm and confident voice.

"A.C., you were a soldier. A loyal, willing combatant who gave his life for his country. That sacrifice was your last full measure, and it should have been met with respect and honor. Instead, people with questionable integrity took it and abused it. They didn't bury you with accolades or put your name on the S.H.I.E.L.D. wall of fallen agents. No, they moved your body off to a diabolical location to torture and brainwash you. They lied to you, and they made you feel that everything you believed in was false. And you wonder why you're confused. You have every right to be." Skye felt torn when she saw the single tear that edged down Coulson's face. But, she had to make him see that he wasn't reacting any differently than any other man would when faced with the same circumstances. And she wanted him to know how much she truly trusted him.

In an almost indecipherable gasp he replied, "I wanted to die."

"And that was what you should have expected, A.C." Skye answered with emotion. "You did your job, and you died for them. No one should have asked more of you."

Reaching up to wipe his tear with a corner of the sheet, she was glad to see him finally meet her eyes. The guarded look he usually gave her was gone. He searched her eyes for anything false, but he saw only real compassion there. And he saw something that he'd always seen from the first time he had met her. He saw her old soul. The same one he had. The one that had been built upon the bricks of life, love, betrayal, loss, struggle and suffering. Yet, he also saw her calm determination, compassion and trust in humanity. He knew with all his heart that he cherished this woman and would never hurt her intentionally.

"Skye, don't do this if you don't want to. Don't do it for me. I would never expect you to." He said.

"I wouldn't, A.C." she replied. "But, this is something I think is right. I don't want anyone else going through what you did. We have to stop this."

They sat in silence on the bed for a long time, holding each other. A common purpose, a common bond had brought them together and it was stronger than most attachments people made with each other. Theirs was born in experience and ideology, and whether it led to something more was yet to be discovered. But, for now, it was enough. More than enough.

To be continued.


	2. Chapter 2

AT LEAST WE'RE IN THE DARK TOGETHER

Chapter 2.

A/N Thank you for the reviews and follows. As someone said, the episode Yes Men bothered them and it did me too. At least until I took a Clark Gregg interview and combined it with the episode and came to these conclusions. Thanks for reading. Oh, sorry for the short chapters, but I want to write something every day if I can.

Skye couldn't sleep so she sat on her bunk and tried to puzzle out some things that had been bothering her. It had been two days since her talk with Coulson. She had passed him in the hallways, but he'd always seemed distant and preoccupied. So she let him be. Simmons, however, had been a virtual fount of information. Her friend had told Skye about AC's medical report. How badly he had been tortured and for how long. Fitz had filled them in about what the place looked like, the evil and painful-looking machines that surrounded the table that they assumed Coulson had been lying on. It was beyond barbaric, and Skye was starting to fully understand his overwhelming need to find out the truth behind what had been done to him.

Simmons also told Skye something else that made the young hacker afraid, not for herself but for her friends, all of them. She said Coulson's moods were all over the place and he became angry and upset frequently. She recounted the incident where she had confronted Coulson about sending in the blood samples to HQ.

"Skye, you would not believe how angry he became. I've never seen him like that." Simmons recounted the tale. "He actually scared me."

Skye knew exactly why Coulson didn't want the samples to go to HQ. If he allowed her to do that, whoever had hurt him was likely to find out that he and his team knew about the alien. Then it was anybody's guess what would happen to them all. She had tried to calm her friend down basically apologizing for AC and his behavior, but she also knew it was unacceptable and that she would have to talk to him about it.

Now, perched on her bed, she began to recall some of his other strange behavior. She knew he very seldom slept or even rested much. He looked almost haggard as he trudged around the bus each day. She had caught him standing alone or sitting in Lola with a faraway look in his eyes like he was seeing something that wasn't there. He was so moody, but also so emotionally distant, almost like he felt that no one cared anymore so why try to be friendly. And, of course, there was his intense need for revenge. That one was so out of character for the man she had come to know as kind and forgiving. What was that?

A need for refreshment drove Skye out of her bed and into the lounge where she was surprised to find the man himself ensconced on the couch, sans coat and tie. He was so engaged in what he was reading that he didn't even notice her entrance. She cleared her throat and he looked up. She was surprised how she hadn't noticed the dark circles under his eyes, and without the jacket she realized that he had lost weight since they'd first met. It felt like watching a heroic statue crumble before her eyes and Skye blinked at the sudden emotion the vision evoked.

"Can't sleep either. What are you reading at this hour?" She asked as she bent to see. It was the dreaded medical report. "Yeah. Simmons told me about this. Why torture yourself with going over this, AC?" She tucked her legs under herself as she settled on the couch next to him.

He shrugged and put the report on the table. Sitting back he looked at her with what can only be described as troubled eyes. "I…have nightmares. Every night." He motioned to the paper. "Sometimes this makes me feel better. Gives me some control, I guess. At least there is a record of what happened even if I don't remember most of it."

Skye couldn't help but hear the pain and humiliation in his voice. "AC, this was in no way your fault…."

"I should be stronger!" He cut her off. Leaning forward, he rested his elbows on his knees and cradled his face in his hands. "It's like I can't forget it, Skye." He mumbled, but she heard him clearly. "I want to, I need to, but the nightmares, the flashbacks…"

"You're having flashbacks?" Skye queried as gently as she could. She knew how scary that had to be for a man who had lived his life always in control, always the rock to which others had clung to in the storm. She put her hand on his back and rubbed, knowing the contact seemed to soothe him. He brought his hands down, but still wouldn't look at her.

"For a while now, yes." He answered as if ashamed. "That's why I get away from the plane. I… don't want anyone to see. I don't know when it will happen." He felt alone, impotent. Why did this happen to him? What had he ever done to deserve it?

Skye sensed his internal struggle, but wasn't sure how to help him. So, she stayed with him, because that's what friends do for their friends who are in trouble. Eventually, he settled back on the couch and closed his eyes. She couldn't tell if he was asleep, but he was resting and that was better than nightmares and flashbacks. She held his hand contentedly until she too, became sleepy. Then she leaned back against him, snuggling into his shoulder and closed her eyes.

The team found them that way in the morning.

To be continued.


	3. Chapter 3

AT LEAST WE'RE IN THE DARK TOGETHER

Chapter 3.

During the night, Skye's hand had migrated between the buttons on Coulson's shirt and rested now on the soft hair covering his flat abdomen. That's the scene that Grant walked in on when he entered the lounge. Whether it was the lingering effects of the Lorelei incident or the berserker staff he wasn't sure, but he became enraged.

"You hypocrite!" The words flew out of his mouth as he saw what to him was a boss who threatened him with reassignment when he found out about May, but was now carrying on a similar relationship with Skye.

Skye's body tensed as she heard the words and the anger behind them. Coulson grunted when she launched herself up using him as a lever.

"Ward, what the hell?" Skye blinked her sleepy eyes and frowned at the large man. Behind her, Coulson stumbled to his feet, unsure of what was happening.

Grant barely controlled his anger as he shouted at his superior. "You've got the balls to discourage me from sleeping with May, but now I find you taking advantage of Skye!" His eyes blazed, and Skye became alarmed.

"Wait, what? He's not taking advantage of me, Ward. There's nothing… inappropriate going on here. We just fell asleep after talking!" Skye explained. She looked around in confusion as Fitz and Simmons came into the room having heard the shouting. Behind her Coulson was sinking into a dark place. This had suddenly become a deadly confrontation in a matter of seconds.

"This is MY bus." Coulson rumbled through gritted teeth. "You don't get to talk to me like that." Ward took a step toward him. The younger agent and his boss sizing each other up for possible strengths and weaknesses. Their violent intentions were obvious in the unwavering stares they gave each other. Skye, Fitz and Simmons watched on in horror.

The sound of two gunshots filled the room. Ward and Coulson dropped to the floor and everyone else's eyes turned to the source of the gunfire. Melinda May stood in the doorway holding the ICER gun.

"Way too much testosterone in here." She said grimly.

Suddenly, the spell was broken and attention turned to the injured men. Ward had managed to fall gracefully onto the lounge chair, his eyes open, but unseeing. Coulson, having been between the couch and coffee table, hadn't faired so well. He had pitched forward and cracked his head on the way down. A pool of blood was spreading slowly around his head.

"Oh my god, AC!" Skye raced to grab a bar towel to try to stem the blood flow. "Help me get him on the couch!"

Between the four of them they managed to lay Coulson on the couch, Skye pressing the towel against the gash on his forehead while Jemma ran to get a med kit. After a few tense minutes, his head was expertly stitched.

"He's gonna have a hell of a headache, but I don't think there's any worse damage." Jemma finally pronounced. She looked around the group until her eyes settled on Skye.

"What happened? Why were they about to throw down?" She demanded.

Skye shrugged her shoulders. "AC and I couldn't sleep last night, so we ended up on the couch here talking. We fell asleep, and I guess I got cold in my sleep and snuggled up to him for warmth. That's all it was. Ward came in this morning and came to the ridiculous conclusion that we had _slept _together. I honestly don't know what else he was going on about. May?"

The older agent's face closed off at the question. "How would I know? It must have been something between them I would imagine." Skye was experienced enough to know a lie when she heard one.

"So," she said tentatively, "keeping some secrets there, May?" Anger flashed in May's eyes as she answered the young hacker.

"There are a lot of secrets on this bus, as you would know." May said tersely before she turned and exited the room.

_She can't possibly know about my pact with AC. _Skye tried to keep her face blank so Fitz and Jemma would not be suspicious. Behind her Ward groaned softly and began to sit up. Jemma went to his side.

"Slowly, Ward. Get your bearings before you move." She cautioned him. He looked over at the couch, taking in the blood on Coulson's shirt and the bandage on his head.

"Oh, damn. Tell me I did not do that." He said softly and with genuine remorse.

"No, but I think you were wanting to." Fitz spoke up. "Why were you so mad at him?"

Ward shook his head. They didn't know about his relationship with May. Seeing Coulson with Skye had set off the internal rage he thought he was keeping at bay pretty well.

"It was a misunderstanding," he managed to answer as he looked at Skye in apology. She wasn't buying it, but remained silent.

Fitz chuckled to break the tension. "Thank god May broke it up with the ICER gun. I think it might have gotten a lot worse."

Ward frowned and stood shakily. "Let me know when he's awake. I don't know if an apology will help, but it's all I can do." He walked from the room. Jemma left and came back with a blanket and pillow which she arranged around Coulson.

"Someone should stay with him. If he doesn't wake up within the hour, I'll have to do a scan to make sure there's no hidden damage." She looked at her friend, Skye. "Why don't you go take a shower and change, I'll stay until you get back." Skye looked down at her AC. This just wasn't fair she thought. He'd been beaten up both emotionally and physically way too much in the last year. She made a solemn promise to herself that she wasn't going to let anyone hurt him anymore if she could help it. Then she left to get her shower. It would be a long day, especially since she wasn't going to let Coulson out of her sight.

To be continued.


	4. Chapter 4

AT LEAST WE'RE IN THE DARK TOGETHER

Chapter 4.

**A/N Thanks for the faves and follows. They mean a lot to me, even though it's just fun to write what I find interesting. Sorry for those who ship other couples, but this is starting to get into "ship shape" if you will.**

A newly washed and changed Skye peeked into the lounge only to find it empty. She reversed track and headed down to the lab where Coulson sat perched on a chair with a pained look on his face. Jemma was carefully removing the blood-stained bandage from his forehead, and she looked up when Skye entered.

"Just replacing it with a clean one." She told Skye when she saw her worried look. "He says he isn't dizzy or nauseous, so I think it's just a superficial injury." She looked down at her patient when he flinched. "Come on Agent Coulson, you've had worse than this."

"I know," he replied. "I guess it's just starting to have a cumulative effect on me." He sighed and stood up when Jemma finished. Skye and Jemma shared a worried look. Coulson got quiet, almost like he forgot they were in the room. His earlier anger seemed gone, and although strangely distant, he seemed more back to his old self. Everyone turned to look when Ward strode in.

"Sir," he began looking beseechingly at his boss. "I take full responsibility for what happened in the lounge earlier. I was so… out of line."

Coulson continued to stare at his shoes as he responded in a soft voice. "It wasn't you're fault, Ward. I'm the one who took it too far. We've both been under a lot of stress. Hell, the _whole_ team is pretty beat up." He looked up at Ward. "I haven't been much of a leader to you all lately and I'm sorry."

And that's when the strangeness happened again. Ward took a step toward Coulson, not at all thinking about how this was backing the older man up into a corner of the room. Ward just wanted to shake and make peace between them. Just as Coulson pulled up into the corner, Jemma accidentally tipped a tray of instruments onto the floor making a very loud clanging sound. Skye happened to be focused on her boss's face and was startled at the instant and powerful expression of anger that erupted there. Everyone stopped in confusion.

"Sorry, sir," Jemma spoke first, but Coulson did not seem to register her words. He began sweating and breathing hard.

_There's that scared rabbit look again._ Skye motioned the others to stay away from him. They watched in concern as he seemed to be seeing something they couldn't. Finally, his breathing slowed, and he seemed to slump in on himself.

"Sorry," he apologized again, but this time Skye was having none of it.

"What are you sorry for AC?" She asked gently. He looked around in confusion, not seeming to remember where he was for a moment.

"Maybe you should sit down, sir." Jemma commented. "Let me do a scan of that head. There may be some internal bleeding…."

"NO!" The anger was flashing in Coulson's eyes again. "Just… just leave me alone. Ok?" He turned and fled from the lab.

"Well, what the hell?" Ward commented. "He's like Jekyll and Hyde lately, and I don't know what to do to help." Skye stepped around the tall warrior and began to follow Coulson out of the lab.

"Skye, be careful." Jemma called. She watched her friend exit with more than one misgiving. Was Agent Coulson dangerous?

…..

Skye waited for a bit in the hallway. Coulson had not noticed that his door was slightly ajar and she could hear him moving about and then the shower running. Looking to see that no one saw her, she slipped into his room and closed and locked the door. Then she waited. A few minutes later he came out of the bathroom dressed in a tee shirt and jeans. He didn't see her at first, and she took the moment to study him. He was so much smaller than Ward, but he was all muscle. She bet that, if measured, his body fat percentage would be less than 10 percent. And, she knew he must be strong by the way his muscles filled out the tee shirt at the chest and arms, but not, like a lot of middle-aged men, at the waist. His jeans fit him tighter than the suit pants, and she was impressed there as well.

_I'm sexually ogling my boss!_ _What's up with THAT? _She looked up to see him fixing her with a pointed stare. Skye couldn't help but think he was unprofessionally sizing her up as well. There was that chronically measured age difference, but in mind and spirit, they were much closer. She realized too, not being a virgin herself, that she was attracted to a man physically not just by youth and smooth skin, but by other less measureable criteria like personality, voice, smell and touch. Right now she was wondering very much what his chest might feel like if she ran her fingers over it.

Clueless, as usual, Coulson took her staring at his chest in entirely the wrong way.

"What? You want to see it?" He asked resignedly. "It's pretty damn ugly. Probably give you nightmares."

_Well, maybe I can put this misconception right. _Skye crossed the room and stood in front of him. Her proximity made him stand a little straighter and she reached for the hem of his tee shirt without ever letting her eyes leave his. He reached down to stop her.

"Okay, I really meant that. It's hideous." He said in an even voice.

"I still want to see." Skye kept her voice just as even.

Coulson sighed. "Why? Can't you just let me have my privacy?"

"It's not your privacy you want AC," Skye replied. "It's your shame. You've convinced yourself that you are unworthy of even being seen." His eyes left hers and refocused on the floor. She knew he heard the truth of her words. Slowly he began to pull his shirt up and then off revealing the scar in all its reality. It's pink and hairless jagged line crossing his heart with what he felt was a symbol of his failure to stop Loki, to help his friends, to save the day.

Skye did not flinch away or show revulsion. She asked him if it hurt to touch it instead.

"You…you'd _want_ to do that?" He was stammering now.

"Yes. It's a part of you now. Just like mine is a part of me. It's not a symbol of failure, incompetence or any other ugly thing. It's a badge of honor, my friend. However you blame yourself for what happened when you got it, you must admit that your intentions were brave and honorable. You are human. You are not a God." She remembered a story he had told her about Thor and continued, "If you remember, Thor had to learn humility to become his true self." She smoothed her hand over his scar and over his heart. "This is not ugly, AC. This is a symbol of your true self, and you have no reason to ever doubt what that is. It's why I love you."

To be continued.


	5. Chapter 5

AT LEAST WE'RE IN THE DARK TOGETHER

Chapter 5.

Skye scanned his face for some kind of emotion. She'd just told him she loved him, and desperately needed not a Coulson mask, but a real response. He had to have heard her. At first his face registered nothing, but as she continued looking at him it morphed into disbelief, concern and finally, hope. Or at least that's the way she interpreted it. But, he still wasn't verbalizing any feelings, and she was starting to get worried.

"Skye," he finally said tentatively, "I know you don't mean that the way I'd like to take it, but thanks for that." He pulled his shirt back on and sat to tie his sneakers.

Skye was more than a little pissed. How did he want to _take_ someone telling him that they loved him? "Okay, AC. Exactly how would you like to "take" me loving you." She said with an edge to her voice. He seemed surprised at her distress, but opted to be honest with her.

"People usually love me for what I can do for them." He explained calmly. "It's just the way it's always been in my whole life. I'm the one who solves the problems and takes the edge off the mistakes. Love, to me, has always been predicated on my skills or behavior." He sighed. "It would… it would be nice to experience unconditional love." Ducking his head down, his voice had been so soft that Skye barely heard the last words. She took a step forward, determined to explore this new side of Coulson that he had just opened up. But fate intervened. A loud pounding on the door interrupted them, and May's voice boomed.

"We've got a mission!"

Coulson strode to the door and opened it. "Where? Is it about the Clairvoyant?"

May took in his casual attire and then looked past him to Skye. For a slight moment Skye thought she saw some unveiled emotion in the older woman's eyes. Then, the moment was over as AC pushed past her on the way to the control room. May and Skye followed.

Fitz, Ward and Simmons were already at the holotable. They looked up in surprise as their boss entered in jeans, sneakers and a tee shirt.

_He looks so human. _Simmons realized for the first time. _Almost like he could actually have emotions like the rest of us._

"HQ has traced the path of the Deathlok device to a small factory in northern Italy." Ward spoke up. They want us to go there and check it out."

Coulson felt the heat rise inside. _Not now, _he thought. The sweating and difficulty breathing was coming on hard, and he had to make a retreat soon. "Okay, May set a course. The rest of you try to come up with whatever you can on this factory." He turned and left quickly.

"Is he sick or something?" Fitz blurted out. The others said nothing and went about their assignments. Whatever was going on with Coulson, they were trying to ignore it. He didn't get sick, and he always came through in a pinch. What was there to worry about? Skye, alone, noticed and committed the incident to memory. She had already began to worry.

The Bus sat grounded at the nearest airfield to the factory. So far, they knew just a little about this place. It seemed the factory had been in use since WWII, and its goods were not sold to anyone they could trace. It was a factory making things that apparently no one bought. Not a good sign. Coulson sent Ward to ascertain the security there and look for possible openings. Skye was tasked with trying to find more information, while Fitzsimmons played with the Dwarves making adjustments that might come in handy. Coulson had changed back into his suit which seemed to settle some nerves. No one was aware of the turmoil that was taking place in the body that was covered by the suit. He was staring off into space again in the control room when Skye found him.

"AC," she said softly, but did not get a response. Touching his shoulder gently brought him back, and he looked confused. "Ward's back." She told him.

"Back?" Coulson frowned. He was having so much trouble concentrating. Thank god it was Skye, she wouldn't make a big deal out of it. He was so tired from not sleeping, the damn flashbacks were becoming a daily thing, and his confusion tended to overwhelm him at times. _I gotta hold it together. _He told himself as he rubbed a hand over his face.

"Ward's ready to brief us on the factory defenses." She explained to him. She didn't bother to ask him if he was okay anymore, because obviously, he wasn't. Instead, she kept a close watch on him and was ready to help when, not if, she was needed. Her AC had become a walking, talking train wreck in progress. It was really only a matter of time. He motioned her ahead of him and followed her to the lounge where the others were sitting. When she sat on the couch, Coulson sat close to her as if sensing she was his buffer against the outside world.

"Well, they've got the usual perimeter cameras," Ward began. "Just on the four corners of the installation. I only saw two doors, in front and back. The factory is built with cement blocks, so the doors seem like the only ways in." He yawned. He had stayed all night to observe the comings and goings at the factory. "There were two dozen men who entered and then left during the day. Since I couldn't see anything inside, there may be more men inside who stay there round the clock. The men enter through the door using an eye scan. Maybe Skye can beat that, I don't know."

Skye responded, "Hey, if anyone can it's me."

May spoke up. "We need to capture one of these men for you, Skye?" The hacker nodded.

"That would make it way easier." She agreed.

"When we're in there we need to grab any files they have." May continued. "This could be our big break that leads us to the Clairvoyant."

"So when do we go in?" Ward asked, turning to Coulson. His superior stared straight ahead, jaw muscles tightening as he spoke.

"After they leave tonight we grab a man for his eyes. Then, when Skye creates our key, we go in." A grim look passed amongst them. Each of them hoping that this would finally be the time they discovered who the mysterious and dangerous Clairvoyant was.

To be continued.


	6. Chapter 6

AT LEAST WE'RE IN THE DARK TOGETHER

Coulson sighed as he pulled the bullet-proof vest on. He knew that this piece of necessary equipment would be forever linked to his horror at seeing the blue alien. Taking a deep breath, he tried to fight down the panic and focus on the mission ahead.

May and Ward had handily kidnapped one of the factory workers so Skye could make an eye scan to get them into the building. She had also put the outside cameras on a continuous repeat loop so anyone watching would not see them.

Now, he, Ward, Skye and May were getting ready to enter the factory to find god knows what. His nerves were so on edge that his hands were shaking. He removed his handkerchief and soaked up the excess sweat on his brow. _This is not what a real leader looks like before a mission. _He glanced around at their small group wondering if anyone had noticed, but only Skye was giving him a concerned look. Forcing a smile, he motioned the team forward to the door where Skye used her magic to operate the scanner. With a soft whoosh the door opened and Skye looked smug. Coulson sidled past her to take the lead, while May brought up the rear. They were on the top floor catwalk that looked down on a factory floor. Various large machines silently observed their entrance, but surprisingly there didn't seem to be any indoor cameras.

"I don't like this." Ward muttered. "Too easy." The team crept down the stairs to the lower floor.

"Split up." Coulson directed. "May, you and Ward check the machines. See if you can tell what they are making. Skye, you're with me." He began to lead her over toward what looked like an office area.

"They're locked." Skye said as she tried the drawer on the file cabinet. Coulson just smirked and reached in his pocket for his favorite toy. He motioned Skye back, placed the small bomb against the drawer lock and then stepped back and turned around.

"Cross your arms," he grinned at Skye. "Keeps the hands safe." The small explosion jarred the drawer open. They stepped forward and looked in. It was completely empty. The word "trap" leaped into Coulson's consciousness. He grabbed Skye's arm.

"Ward, May! It's a trap!" he yelled. "Get out of here!" They met the two other agents at the stairs. "Go!" They were only halfway up the stairs when the gunfire started. Ward leaped to the catwalk and began firing down toward the source of the bullets. May joined him and was soon joined by Skye.

"I see them," Ward touched May's arm. "Behind that yellow half-wall. You go left and I'll go right. Skye, stay here behind that cement post. You'll be safe there. These guys are really bad shots!"

The two agent split up and soon after Skye heard more gunfire and then silence. Ward and May rejoined her.

"All clear," Ward said. "It looks like there were only two of them. How did Coulson know it was a trap?"

"The file drawers were completely empty," Skye replied. "Someone knew we were coming. Maybe that worker we kidnapped was supposed to check in with someone?" Ward nodded. It made the most sense. He and May had only discovered machinery, but not a single piece of what was being made.

"Where's Coulson?" May asked and they all looked around.

"He was behind me." Skye looked worriedly down the stairs. "What… oh, god. Is that blood?" She was looking at the floor near the bottom of the steps.

They rushed down and followed the blood spatters around a concrete wall. Coulson sat with his back braced against the wall, his right hand pressed against his abdomen below the vest. Red blood was seeping between his fingers.

"Nooooooooooooo…" Skye moaned as she dropped to her knees beside him. "AC? Talk to me, please!" He opened his eyes and gave her a weak smile. "It'll be alright, Skye." He said softly, but to her his meaning was clear. "You are NOT going to die on me!" she said firmly.

"Sir, can you walk?" Ward got on Coulson's other side and helped Skye bring their injured boss to his feet.

"The steps are gonna be tough…" he complained weakly, but the other agents were not going to leave him and they wrestled him up the stairs and back to the Bus. Jemma had been apprised as to what was going on. She had the med bay prepped and ready. Quickly, Coulson was relieved of his jacket, vest and shirt. Jemma pulled up his tee shirt to reveal a small bullet wound in his lower left side.

"Good news is that it's a small caliber round." She said. "Bad news is that it's still in there. You're going to need surgery, Sir. May, how fast can we be back at a S.H.I.E.L.D. medical facility?" Her words were a catalyst for Coulson.

"NO!" He shouted. Using what little strength he had, he swung his legs over the side of the bed and staggered to the corner of the pod, as far away from them as he could get. "I won't go back there. Don't make me go back there!" His voice bordered on hysterical.

While the others looked on in dismay, Skye and May exchanged knowing looks. "Skye, get him back in bed. The rest of you outside." May instructed them.

Outside the pod, Jemma confronted May immediately. "That bullet's got to come out, Agent May. He'll bleed to death if it doesn't."

May nodded. "I know that, Jemma. But I'm going to be honest with all of you right now." She took a moment before she continued gravely. "What I'm about to tell you is way above your clearance level. Even Coulson doesn't know. After he was "experimented" on, the doctors warned Director Fury that the ramifications of that experience were definitely not over. Agent Coulson has developed severe emotional problems from that trauma."

"Post traumatic stress disorder." Jemma supplied quietly. "Of course. The signs are all there."

May nodded. "What you don't know is that I was assigned to watch over him. I report to Fury himself." She watched the shocked looks form on the faces of her coworkers.

"You're _spying _on him?" Fitz angrily asked.

"Yes." May replied simply, but then elaborated. "Fury wants very badly for Coulson to recover properly. He, and I, thought that getting him back into the field was important. We were, _are_ sure that he can do it. But, this is a setback. He is literally terrorized by the thought of being in the hands of S.H.I.E.L.D. doctors again. I can't blame him there." She looked at the stunned group.

"I know right now you all think I'm reprehensible," she motioned toward the pod where Skye had managed to get Coulson back on the bed. "But, for his sake, can you wait to castigate me? Jemma, is there any way _you_ can get that bullet out? He trusts you."

Jemma was astonished and more than a little afraid, but she raised her chin and spoke clearly. "I'll do my best, Agent May." She replied. When Fitz started to argue, she shushed him. "This is for him," she told her best friend quietly. "Will you help?"

Fitz nodded. "I'm always on your side, Jemma."

She looked around at the little group. "Then let's get at it. I'll need…"

To be continued.


	7. Chapter 7

AT LEAST WE'RE IN THE DARK TOGETHER

Chapter 7.

**A/N Thanks to all who have reviewed, favored and followed. This chapter contains some medical material which I know practically nothing about so bear with me. Sorry if it isn't completely realistic. **

Jemma stood next to Coulson as he lay on the bed. May was on the left and Skye on the right holding his hands. He still looked terrified, especially when Fitz brought in the portable scanner.

"Sir," Jemma stated gravely. "I can't just go carving on you like a side of beef. We've got to use the scanner to pinpoint the exact location of the bullet. Otherwise you'll lose too much blood and the chance of infection goes way up. Okay?"

Coulson, for once, was not the man with all the answers. He was lost and in a lot of pain. His eyes sought out the one person he trusted implicitly – Skye. She met his eyes and in a gentle voice responded to his unspoken question.

"I'm right here. Not going anywhere. Please let them do this, AC." Everyone let out a sigh of relief when he nodded yes, although Skye and May noted the increased pressure on their hands where they held his. This was traumatic for him, and Skye hated that. She hated what Fury had done to him, but now was not the time for that.

Skye reached over with her free hand and cupped Coulson's face. She turned his head toward hers and away from the scanner. "That'ta boy, AC. Look at me. Did I ever tell you about the time I went skinny dipping on a golf course?" This statement not only pulled Coulson's attention off the scanner, but perked up the ears on Ward and Fitz as well. May just gave a little smile of appreciation for her younger colleague.

"Well," Skye continued, "it was a scorching August night in New York. My boyfriend…NOT Miles at the time… and I were burning up and the van's air was on the fritz. So we snuck onto a private course and ditched our clothes. Damn that water felt good. I didn't think until afterwards what other life forms were probably in the pond with us." She shivered, noticing that Coulson was totally ignoring the ongoing scan. "Afterwards, we got out and laid on a blanket to dry. It felt good being, you know, _naked _outdoors and gazing at the stars. Of course, then we….."

"Finished!" Jemma almost shouted. "And just in time." She mumbled under her breath. Shoving the scanner toward a dazed Fitz, she told the rest of them to wait a few minutes.

"Nice story." May grinned at her. "It definitely did the trick." Skye smiled and gave Coulson's face one last caress as she removed her hand. Leaning down, she placed her mouth right next to his ear and whispered so only he could hear.

"I wish you were the one that was with me then." She sat back up and reveled when his eyes got wide and he gripped her hand in response. Even though she truly meant it, she could always claim she was just distracting him at the time if he considered it inappropriate. Jemma chose then to return.

"Really good news." She said almost cheerfully if that was even possible in this situation. "The slug is resting only an inch below the skin next to your hip. It should be easy to remove and stitch up. You ready?" She pulled out a large syringe. Coulson gulped, but nodded to go ahead.

Jemma explained, "This will numb up the area, but don't worry, you'll be awake for the whole procedure. You've got to hold very still though. Okay?"

"Go ahead," Coulson confirmed in a weak voice. He groaned softly, but held very still as she injected him with the numbing agent. After waiting for it to take effect, Jemma took a small scalpel, located the area where the bullet was and made an incision. With gloved hands she reached gently in and easily slipped the projectile out. She poured anti-bacterial medicine in and around the incision, and then she quickly used stitches to close the wound. She wiped everything down again and used fresh bandages to finish.

"That should do it." She said confidently. Looking at Coulson, she said "I'd prefer you rest here for a while. This is much more sanitary than your quarters." Coulson blinked, but his face was determined.

"I'm fine." He said as he tried unsuccessfully to sit up. The anesthetic was beginning to wear off and his side felt like it was on fire, but the clinical appearance of the place was still bothering him. Skye gently pushed him back on the bed.

"I'll stay with you here." She said simply, hoping he would agree, needing him to agree. She wanted to talk to him about things that had come up recently. It was important to her that he know what was going on. This was his life, and she understood completely how it felt to be lied to. She was not going to be a participant in that. Luckily, he was too hurt and exhausted to put up much of a fight.

After the others left, Skye ran her hand over her AC's forehead and cupped his face again. Looking into his eyes, she tried to establish if he was awake enough to hear what she had to say.

"Skye, what is it?" he had noticed the troubled look in her eyes. She swallowed and worked up some courage for this conversation.

"I've just learned something, and I want to tell you. But, I can wait if you need to rest for a while." She didn't want to delay, but she respected his needs.

"Tell me." Coulson looked again like he was resigned to hearing more bad news, and Skye's heart broke that she had to deliver it. She quietly and succinctly told him what May had revealed earlier. His eyes filled with tears that wouldn't drop. They were tears of anger, betrayal and shame. He didn't question Skye's narrative, he trusted her implicitly.

"So…what… I'm crazy?" he finally managed to get out.

"No, AC! Don't ever think that. I read a lot about this. You have what are called '_moral wounds_.' You have all your life believed in doing what's right for your country and for your fellow man. You've lived by the S.H.I.E.L.D. code. But, now you are forced to realize that things are not so black and white. That morality is subject to manipulation, and that those you trusted betrayed and hurt you." She huffed in frustration at the situation. It wasn't fair to him, but it had happened and couldn't be redone. All she could do was to be there for him. "They pulled your symbolic rug out from under you, AC. Your life is changed forever by psychological wounds that may never heal. And now, they want to make it all better by lying to you."

Coulson was shocked and her words made his heart thump in his chest. "It won't get better?" he asked.

"Especially if they continue to lie to you, AC." Skye leaned forward and rested her head on his chest. It felt comforting, and he laid his hand on her back. He had a lot to think about. He knew May was his friend, even though she was actually participating in what S.H.I.E.L.D. was doing to him. For the first time in his life he feared for his sanity. He felt lost and conflicted about what was happening to him and how he should deal with it. But, one thing he knew was that there was one person who understood it all, and that was this girl in his arms. He drew her tighter to him and let himself succumb to exhaustion.

To be continued.


	8. Chapter 8

AT LEAST WE'RE IN THE DARK TOGETHER

**A/N Well, we're finally at the end of this story, but if people want to read more, let me know and I'll continue with a new story. This just felt like a good place to stop this one. Thanks again to all who read and reviewed, followed and faved. This is such a great show, isn't it? Take care, all!**

Chapter 8.

The next morning Skye sat patiently at Coulson's desk waiting for him to finish his shower. She knew he was at a very low spot in his life, and she wasn't about to let him go through it alone. A few minutes after she heard the water shut off he entered the room dressed in faded blue jeans and a v-necked sweater. Surprised and smiling, she teased him gently.

"Didn't know you owned anything that didn't look brand new." She told him. He glanced at her and made an attempt to smile, but failed miserably. She noticed him struggling to tie his sneakers and bent down to help. He sighed, frustrated.

"I'm not _five._" He said crankily. Skye ignored him and finished tying. Then she stood up and faced him.

"No, you aren't." She said patiently. "But, you need a little help in your life right now. I know you've always stood alone, AC. This time, however, you've got some help – me. And I'm not going anywhere because I do love you, whatever that may mean to you. Deep down I think you know how this is supposed to work. You're just too stubborn to admit that this time _you_ are the recipient of the support, not the giver of it." Her words seemed to strike a hidden chord in his psyche. His face took on an open, starkly lost look. She stepped forward without thought and placed her hands on either side of his face. Not hesitating a moment, she brought his head down and kissed him. When he didn't pull away, Skye took it as a sign, and deepened the kiss as she pressed her body into his and she felt his arms go around her. When they both finally needed air, she felt him step back and he looked at her uncertainly.

"Skye, I can't handle pity right now." He said slowly and deliberately. He wanted to be as honest as he could with her. Skye smiled and ran her hand down his chest to his waist.

"Is it pity when I adore your smile? Or when I'm standing close to you and just your smell makes my knees weak? Is it pity when I crave your touch?" She told him. He looked surprised.

"You…you could have any man you wanted." He said simply. "Handsome, tall…. younger." He didn't get it yet.

"AC, I know in books and movies that's how it always seems to go. But, I'm telling you that not all women are after that, are turned on by that." She smiled at him. "When you solve complex situations by putting several different variables in the correct order, I am turned on. When you talk to a man who is going to die and try to make him less afraid, it turns me on. When you are compassionate to your coworkers and fight for them even if it gets you in trouble, it excites me. It's what you've made of yourself, Phil Coulson. Not what you look like, even though from what I've seen that's not too bad either."

She smoothed her hands around his torso and grinned when he groaned softly. They came together again in a much more passionate kiss.

"The door's locked." She whispered sweetly in his ear and that was pretty much all it took. He broke away from her to hit the button that folded out his bed. Then with great care he undressed her and she him. It wasn't a hurried thing. They stopped to enjoy each other's bodies along the way. His incision on his hip was small and healing. She discovered that his scars were sensitive, but not painful for him. He carefully avoided touching her deeper, healing wounds. She discovered what a thorough lover he was, as he enjoyed giving her pleasure as well as enjoying what she gave him. It was tender, sweet and life-affirming. It was what they both needed.

…

"Well, I'm glad that creep is out of here." Fitz said as he watched the S.H.I.E.L.D. team take the factory worker off the bus and into custody. "It's just a shame we couldn't find anything at that damn factory."

"I wish Agent Coulson would come down." Jemma said looking up. "I want to make sure that wound is healing well."

"He'll be fine, Jemma." Ward said gently. He knew how much she worried about them all and felt responsible. He was still a little put off that Coulson had been so adamant about not going to a medical facility. He himself, had been tortured at one time, but it hadn't left him a mess like the older agent seemed to be. "Where's Skye?" he said tersely.

May shot him a look. She knew what he was trying to do and she would have none of it. Just then the computerized phone on the holotable buzzed. She was closest, so she hit the button to answer.

Director Nick Fury appeared on the vertical display looking larger than life.

"May," he said looking at the team with his one eye. "I need you in New York."

"Yes, Director Fury," May replied. "Did you want to speak with Agent Coulson, sir?"

"Not necessary." He replied firmly. "How long?" May calculated quickly.

"Three hours, sir." She told him.

"I'll need to talk to you, Coulson and that _consultant. _Make sure they appear, May." Fury's face disappeared as he disconnected the call. Everyone looked around uneasily.

"Are they going to be in trouble?" Jemma asked worriedly.

May just looked blank-faced. Coulson and Skye took that moment to appear. He was back in a fresh suit and she looked freshly showered and somehow different. They both seemed more relaxed than they had in a long time.

"What's up?" Skye asked, raising her eyebrows at the serious group.

"Nick Fury just called." Fitz informed them. Skye felt Coulson stiffen beside her.

"What did he want? Why wasn't I informed?" he demanded.

May reached out and touched his arm trying for reassurance, but not succeeding. "He said he didn't need to talk to you." She said gently. "Come on, everyone. Wheels up in five."

Fitz, Simmons and Ward shot darting looks of concern at their boss before leaving to strap in. Skye knew now was not the time for touching. She moved into the lounge, which was empty, to secure herself. She hoped he'd follow, but was letting him have his space. With a wave of relief, she watched as he came into the room and settled himself next to her.

Knowing exactly what was going through his mind, she braced for a response and wasn't surprised at his sudden sweating and forced breathing. This was one of his triggers she knew. Being forced by Nick Fury to do something that he had no control over. She gently rubbed his shoulder while she silently waited for the attack to pass. His breathing gradually slowed down by the time they were in the air, but Skye was glad no one had joined them in the lounge.

"What's going on in there?" She asked gently as she smoothed the hair on his head back.

"This…this might be it." He replied softly. "Nick wants to check with May, and she'll tell him that I'm no longer fit to command."

Skye realized how terrifying that thought would be to the senior agent. Something he'd spent his whole life committed to, about to be taken away. She struggled with the unfairness of it. He had died a hero and they had forcibly brought him back to life, tortured him, given him some kind of alien infusions, and they knew he wasn't ready for command, but they decided to experiment with his life knowing he would continue to suffer from psychological trauma. It was so painfully obvious to her that Nick Fury and company didn't give a shit for this man.

Skye sighed. "AC, I can't change anything they may want to do to you. But, I can promise you that I'll never leave you." He looked at her, wide-eyed at her promise.

"Seriously," she told him, "they can make you the garbage man at S.H.I.E.L.D. headquarters and I'll become a waitress so we can stay together." His eyes misted at her heartfelt promise, but there was also fear in them.

"But, I know too much." He said softly. "Maybe their plans for me won't include giving me any sort of job." Skye's spine twisted in realization at that. She leaned in and kissed him deeply.

"Then we'll disappear." She said firmly. "Between the two of us, I know we can do it. Promise me, AC. This won't break us up." He looked into her eyes and felt comforted and fearful at the same time.

"Skye, you have your whole life ahead of you…." He started to respond, but she stopped him.

"A life that would be empty without the man I love. AC, you know loneliness. I'm not lonely with you, I'm happy." Tears began to run down her cheeks. "Don't take this away. Don't you leave me too. Please!"

His thumb came up on its own accord to brush her tears away. This was it. He could make the sacrifice and let her go in the hopes that she was young and would find someone else. Or, for the first time in his life he could choose to take what he wanted. To take the comfort, happiness and life that had always been denied him.

"Skye…. I love you." He said simply. The implication was not lost on her. He had chosen her and she smiled with pure joy.

The plane smoothed out, and the others wandered into the lounge. Things took on a normalcy that Skye and Coulson basked in for now. They put the future on hold for a few hours and laughed and talked with the others. For the first time in a while, things were back to the usual. But, not for long….

The End.


End file.
